Re: [gmx-users] Segmentation fault (core dumped) error during minimization

that bound covalently to a ligand. I think there is something wrong with the bond length between N of amino acid and the C of the ligand. How can I find the correct bond length? > On Apr 20, 2020, at 1:08 AM, Elham Taghikhani wrote: > > Thank you > I corrected the mdp file. A

Re: [gmx-users] Segmentation fault (core dumped) error during minimization

with minimization separately. > On Apr 19, 2020, at 11:13 PM, Elham Taghikhani wrote: > >  > Hi > > I am simulating a protein-ligand system, using oplss force field but i got > this error during minimization. > > Steepest Descents: >Tolerance (Fmax) = 1.

[gmx-users] Segmentation fault (core dumped) error during minimization

Hi  I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. Steepest Descents:    Tolerance (Fmax)   =  1.0e+03    Number of steps    =    5 Step=    0, Dmax= 1.0e-02 nm, Epot=  1.27151e+33 Fmax= 4.76291e+07, atom= 1996 Segmentation

Re: [gmx-users] Problem with pdb2gmx

Hi Yes the spacbond.dat and residuetypes.dat files are in my oplsa folder in my working directory. When it gives me topol.top file, it has another name (other_chain B) not FL. I think thats why it doesn't recognize my ligand as a Residue. > On Apr 11, 2020, at 11:25 PM, Elham Taghikhani wr

Re: [gmx-users] Problem with pdb2gmx

    DNA DC    DNA..This is part of my residuetypes.dat file. I think there is some problem with my residuetypes.dat file but i don't what it is. nothing works i am so confused now. On Saturday, April 11, 2020, 8:46:55 PM GMT+4:30, Elham Taghikhani wrote: Thank you for your suggestion. I

Re: [gmx-users] Problem with pdb2gmx

edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully On Saturday, April 11, 2020, 2:08:47 PM GMT+4:30, Elham Taghikhani wrote: Hi Thank you for your response. I added my ligand pdb file to the protein pdb file, then the ligand name

Re: [gmx-users] Problem with pdb2gmx

...         - PLEASE NOTE You have successfully generated a topology from: complex.pdb. The Oplsaa force field and the spc water model are used.         - ETON ESAELP On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani wrote: Hi Thank

[gmx-users] Problem with pdb2gmx

Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. In the topology, I got this warning message :

[gmx-users] Equilibrium state

Dear all, How can we find out the equilibrium state is reached after 20ns NVT simulation? Do the potential energy plot confirm the equilibrium state? or other analysis is required to prove the equilibrium state? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Fw: Radial Density Profile

Hi Salman, Thanks for your response. - Forwarded Message - From: Salman Zarrini To: "gmx-us...@gromacs.org" ; elham Sent: Saturday, November 30, 2019, 03:42:13 AM UTCSubject: Re: [gmx-users] Radial Density Profile Hi Elham, In general to calculate the radial densi

[gmx-users] Coulomb and vdW energies

Dear all, I want to obtain the coulomb and vdW energies between two atoms of separate molecules, However  the .edr output calculate coulomb  and vdW energies of whole system. There is not any option(like -n .ndx) to define the the special atoms in the gmx energy command. How can I calculate the

[gmx-users] Fw: Fw: Radial Density Profile

Dr. Dallas Warren,  Thanks for your assistance. - Forwarded Message - From: Dallas Warren To: GROMACS users ; elham Sent: Friday, November 29, 2019, 08:59:45 PM UTCSubject: Re: [gmx-users] Fw: Radial Density Profile Apologies for mis-reading your question. You need to look

[gmx-users] Fw: Radial Density Profile

function.I can plot the density profile versus X, Y and Z direction.My question is, how can I plot the density profile of an atom versus r?Best regards  - Forwarded Message - From: Dallas Warren To: GROMACS users ; elham Sent: Friday, November 29, 2019, 11:41:07 AM UTCSubject: Re

[gmx-users] Radial Density Profile

Dear all, I am working on vesicle structure of surfactants in water. I want to calculate the radial density profile of surfactant headgroup atoms versus r. The head group atoms are located on the vesicle surface.How can I plot the radial density profile of headgroup atoms from the center of

[gmx-users] (no subject)

Hi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] ATB server (charge assign)

<https://atb.uq.edu.au/download.py?ffVersion=53A6=rtp_uniatom=HEAD=top=26014> will be (*.itp)topology file Is it right? 3-coud you please tell me, when i should get those files (*.pdb and *.itp)? before include proposed new files in my directory or after that? Regards elham Warning! This molecule

[gmx-users] acetaminophen charges

Dear GMX usere my problems is in the assigning the ligand charges in protein-ligand simulation (for instance :acetaminophen ) i acquired (*.itp ) file by PRODRG (after optimization by gaussian software) and ATB server as below. which one is appropriate to my MD simulation by gromaces: *atom*

[gmx-users] charge assign

it to gaussian software to determination the charge of atoms. Is it correct? or i should adding hydrogens to my ligand by another way? Regards elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

[gmx-users] charge assign acetaminophen

Dear GMX users; would you please help me about assigning the charges of my ligand (acetaminophen) for entrance to simulation i'd like to use the groups in aminoacids.rtp file in my force field (gromos53a6) but i don't know how extract my charges thanks elham -- Gromacs Users mailing list

[gmx-users] protein simulation

Dear GMX users i want to compare binding free energy between experimental and MD computations In experimental methods, we assumed that all atoms of a protein that binding to ligand, butin MD simulations, we just assume the sections of subdomain(s) that binds to ligand Is this way correct to

[gmx-users] trjcat

Dear GMX users i ve simulated a system with 1500 steps in md.mdp file and every 3000 steps save the coordinations, thus we have 5000 frames i know i should use *trjcat* for reduce my frames, but i dont know how? for instance for reduction to 500 frames, please guide me about that regards --

[gmx-users] trjcat

Dear Thomas i really apprciate for your advice in trjconv -dt NEW_TIME_STEP_IN_ps. you mean place my new time and my new steps of simulation instead of for example 1500 steps please clarify your mean how i can resolve my problem for changing my steps from 15milion steps (5000frame) to 500

[gmx-users] g_mmpbsa time

Dear users i simulated a system for 30 nano-seconds(dt=2fs) and my frame was 6 ps for binding free energy computations by g_mmpbsa method in gromacs, my computations took a long time is it correct? can i change my simulation time in *mdp* file for *tpr* production for using in g_mmpbsa

[gmx-users] topology making by ATB/PRODRG

elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

[gmx-users] No such moleculetype

appriciate for any help elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se

[gmx-users] adding hydrogens to pdb file

help elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

[gmx-users] binding free energy

Dear Users for g_mmpbsa installation (by using source code and APBS 1.4 and gromacs 4.6.7) after below command: pdfco@pdfco-X:~/g_mmpbsa/build$ cmake -DGMX_PATH=/opt/gromacs \ -DAPBS14=on \ -DAPBS_INSTALL=/opt/apbs \ -DCMAKE_INSTALL_PREFIX=/usr/local/bin/g_mmpbsa \ .. i saw: -- The C compiler

[gmx-users] g_mmpbsa

Dear GMX Users is there anyone to help me in g_mmpbsa using for binding free energy calculation i have questions about *.mdp files as polar.mdp or for instance: what is the value of pdie in protein-ligand combinations i really appriciate for any help -- Gromacs Users mailing list * Please

[gmx-users] Fwd: [g_mmpbsa] istallation Gromacs 4.6.7 Error

/build/CMakeFiles/CMakeError.log. how can i solve it? i really appriciate for any guid elham -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Gromacs 4.5 or 4.6???

Dear Users can i install both of versions of gromacs (4.5 and 4.6) on my ubuntu 14.04 or not? my another question is; can i install vmware along with ubuntu (consist of gromacs 4.5) on my machine (my machine has ubuntu 14.04 and installed GRomacs 4.6 on it) Regards Elham -- Gromacs Users mailing

[gmx-users] g_mmpbsa

OF THE POSSIBILITY OF SUCH DAMAGE. :-) g_mmpbsa (-: Setting option -pdie more than once!Illegal instruction (core dumped) please advise me as soon as possible Regards Elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] g_mmpbsa

Dear Leandro i really appriciate for your help i used of *Pre-compiled binary* http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html#binary for my work and also i did them without -*pdie*, but i saw that error again. should i change the number of -*pdie* or not? i saw in Input

[gmx-users] increase the concentration of protein or drug

not get any compelete response. I really appriciate if somebody can advice me in thus issue. Regards Elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support

[gmx-users] the study of concentration effect in gromacs

Dear Tsjerk thanks for your advice you mean , if i do my simulation in cubic box (1*1*1 nm3)... Now, for twice of concentration, i should simulate for example in cubic box (0.5*0.5*0.5 nm3)? or for instance, i simulated on a system using *2i30* pdb file (Aspirin+Salicilic Acid) that including

[gmx-users] the study of concentration effect in gromacs

Dear All i know for increasing ions in gromacs, we have to using GENION tool but i dont know how increase or change * the protein* or drug concentration in gromacs. i ll really apriciate for any response -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How can i save all run processes ...

or...???) overall, all details in my terminal page regards elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests

[gmx-users] preparing pdb file

Dear Gmx users i have problem with making pdb(s) of proteins that have 2 chain or more. my question is: if in a protein, the active site for two of them (chains) are the same and there is not any advantages one site to another site in chains...which one is choiced?chain A or B? for example: in

[gmx-users] choosing appropriate force field

Dear Justin thanks for your help i used of *ATB server* for making *.itp* file for SAL (salicylic acid), as below: [ moleculetype ] ; Name nrexcl _N4Y 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1OA1_N4YO101 -0.546 15.9994

[gmx-users] charge distriburion

Dear Justin thanks for your replys one of my most important problem is choosing correct pdb in RCSB , there is not any pdb that consist of *Aspirin *+ HSA...and in literature, using of *2i30* as pdb my question is; should we use *docking software* for adding real Aspirin on HSA or we can adding

[gmx-users] farticle demanding about Small-Molecule Topologies

Dear Dr.Lemkul would you please send me full text of your below article : Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies unfortunately, i dont have accessible to full text of this article thanks a lot -- Gromacs Users mailing list * Please search the archive

[gmx-users] pdb information

Dear GMX users i d like to know about pdb information for instance, when i defined concentration of an ion by genion (-conc), gromacs added ion(s) to my structure Now, my question is: in a pdb e.g. (1ZE9: Amyloid beta peptide+Zn+2), there is only one cation in pdb file i want to know about its

[gmx-users] charge distribution

Dear Justin thanks a lot for your response, your answers were very clear As you said,for building blocks i cant use of protein force field and i have to get from the literature(s) would you please recommend me some literature that i can use them? cheers -- Gromacs Users mailing list * Please

[gmx-users] pdb information

Dear Justin i choosed *Cubic* box for amyloid beta peptide+Zn ion simulation for this reason, my *volume* is defined if i suppose that, Zn ion = 1 mol its concentration will be calculated my assumption is correct? cheers -- Gromacs Users mailing list * Please search the archive at

[gmx-users] charge distribution

Dear Justin i really appricite for your help i want to tell all did work until now, again: 1.total charges in my topol.top was +2, then by genion, i added 2 CL to my comlex (HSA+Aspirin) 2.My .itp file (produce by PRODRG) was(consist of 11 atoms) : [ moleculetype ] ; Name nrexcl SAL 3 [

[gmx-users] core dumped

Dear users when i simulated Aspirin on Human serum albumin (pdb: 2i30) in equilibration process (NVT), i encountered with below message and my simulation stopped. i dont know why? *pdfco@pdfco-X:~/Aspirin$ tail nvt.job-nex int0 Number of random exchanges to carry out

[gmx-users] charge distribution

Dear gromacs users i d like to know about charge distribution in .itp file that how can fix the charge of atoms for instance, i simulated Aspirin in Human serum albumin, and i want to know about their charges in an article charge distribution was as below, but in my .itp file (aquired by PRODRG

[gmx-users] core dumped

Dear Justin thanks for your advise only my remained question is, if my problem was for my topology file (as i recieved this error a few times: your topology file has non-zero charge = -0.61) by editing my topology file (.itp file), can i going on my simulation? please tell me, what is the

[gmx-users] free energy problem

by values by us...is it correct? best regards elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https

[gmx-users] free energy question

about writing and accessing to job_*.sh? Could you please advise me Thank you Elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] free energy for ethanol

files for every lambdas... could you please send me some tutorials for practicing this issue (Free Energy Calculation)? best regards elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] free energy calculation

this way.but my received files were empty Please help me Regards Elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests

[gmx-users] free energy of methan

Dear users in attached *.mdp* file, if i replaced *init_lambda_state=0.05 , 0.1 , 0.15* , ... instead of *0* for* lambda=0* is correct? i didnot see foreign lambda in this mdp file.where i include foreign lambda??? regards elham tazikeh *mdp file for lambda=0* ; Free energy control stuff

[gmx-users] error in free energy calculation

Dear Justin when I am doing this tutorial *sh mklambdas.sh run.mdp topol.top equil.gro* I got following error: *mklambdas.sh: 12: mklambdas.sh: Syntax error: ( unexpected* How can I fix this? Best regards, elham -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] perl script running

Dear users how can i running perl script files in my linux ? is this correct? chmod +x *.pl perl ./ *.pl *.xpm thanks for your reply -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] scount.xvg analysis

Dear Justin thanks for your reply is there any script for my problem? i heard there is ss.pl file for this issue,but i don, t have it. could u please help me?! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] (no subject)

Dear users i used of *g_saltbr* for Amyloid Beta Peptide with Zinc cation simulation and aquired 3 outputs :min-min.xvg, plus-min.xvg , plus-plus.xvg there are 5 salt bridges between His 6 , Glu 11 - His13 , Glu 11- His 14 , Glu 11- His 13 , His 14 and also between Asp 23 , Lys 28 in this issue,

[gmx-users] g_saltbr analysis

Dear users i used of *g_saltbr* for Amyloid Beta Peptide with Zinc cation simulation and aquired 3 outputs :min-min.xvg, plus-min.xvg , plus-plus.xvg there are 5 salt bridges between His 6 , Glu 11 - His13 , Glu 11- His 14 , Glu 11- His 13 , His 14 and also between Asp 23 , Lys 28 in this issue,

[gmx-users] scount.xvg analysis

Dear Users i,d like to have a figure , *residue numbers* vs* the percent of alpha-helix, beta-sheet and other secondary structures* but i can not plot them... is there any way to solve my problem? thanks for your favor -- Gromacs Users mailing list * Please search the archive at

[gmx-users] No such moleculetype ZN

it,s related to my version pf gromacs 4.6.5 or not?* *Regards* *elham tazikeh* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un

[gmx-users] No such moleculetype ZN

Dear Justin Please ignore my previous questions. I want to do 2 md simulations: 1) protein and Cu, 2) protein and Zn. After checking force fields in gromacs 4.5.3, I found oplsaa in which there are both Cu and Zn ions in atomtype.atp file. Then I used gromacs 4.6.5 (with opls force field) to

[gmx-users] (no subject)

Dear Users I simulated Zinc ion on human growth hormone protein by Gromacs 4.6 and encountered with this message: there are not molculetype for Zn this sentence means I can not simulate this system on Gromacs 4.6 and have to install version 4.5 on my system or not? regards elham tazikeh

[gmx-users] genion

dear users i studied on amyloid beta peptide with zinc cation and i choosed 1ze9 as my pdb file can i assume Zn without charge in protein simulation alone, or i have to using the amyloid beta peptide alone as pdb for instance,1iyt??? best wishes -- Gromacs Users mailing list * Please search the

[gmx-users] g_covar

Dear users in my anslysis ,i did g_covar and encountered to this note: (the fit and anslysis group are identical while the fit is mass weighted and the analysis is not making the fit non mass weighted) is this important note or not? thanks for your reply -- Gromacs Users mailing list * Please

[gmx-users] pbc problem

dear gromacs users i did simulate zinc and copper ion on human growth hormone protein when i saw my md.gro and md.xtc files by VMD software i found out my system isn,t in the box(cubic) i tried to solve this problem by : trjconv -f md.xtc -s md.tpr -o new.xtc -n index.ndx -pbc mol but there is

[gmx-users] dssp installation error

dear gromacs users when i run do_dssp program 4.5 and 4.6 i saw below error plz help me progran do_dssp, version 4.5.3 source code file:do_dsso.c, line: 521 fatal error: failed to execute command: /usr/local/bin/dssp -na dd5iLsk0 ddj8721A /dev/null2 /dev/null best regards elham tazikeh

[gmx-users] protein simulation

is appropriate for this simulation...isn,t it? best wishes elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] RMSD

Dear gromacs users Can somebody tell me how to calculate the RMSD of the peptide conformation relative to the NMR structure? Best wishes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] force field

Dear friends who knows about force field choosing in zinc ion complex with amyloid beta peptide protein??? i,m looking forward to your reply thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] force field

is appropriate for this simulation...isn,t it? best wishes elham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] Invalid order for directive bondtypes

Dear all I am working on simulation of hydrogen adsorption on graphene sheet, and I need to adopte my force field parameters, new force field folder is made and put in top directory of gromacs. For this reason, I modified charmm27.ff and included new files (bond.itp, nonbond.itp, n2t,